Update R-CMD-check.yaml

xihaoli · Dec 11, 2023 · addd956 · addd956
1 parent a55d856
commit addd956
Showing 1 changed file with 14 additions and 14 deletions.
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -8,24 +8,24 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
+      - name: Install macOS system dependencies
+        if: runner.os == 'macOS'
+        run: |
+          brew install imagemagick@6
+          brew install libgit2
       - uses: actions/checkout@v3
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: 4.2.3
-      - name: Install BiocManager
-        run: |
-          if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
-        shell: Rscript {0}
-      - name: Install GENESIS, GenomicFeatures
-        run: |
-          BiocManager::install(c("GENESIS", "GenomicFeatures"))
-        shell: Rscript {0}
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes", "rcmdcheck"))
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_github("xihaoli/STAAR")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            bioc::GENESIS
+            github::xihaoli/STAAR
+            any::rcmdcheck
+          needs: |
+            website
+            coverage
       - name: Check
         run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error")
         shell: Rscript {0}